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- PDB-4m4w: Mechanistic implications for the bacterial primosome assembly of ... -

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Basic information

Entry
Database: PDB / ID: 4m4w
TitleMechanistic implications for the bacterial primosome assembly of the structure of a helicase-helicase loader complex
Components
  • DNA primase
  • Primosomal protein DnaI
  • Replicative helicase
KeywordsREPLICATION / primase / helicase loader / DnaB / DnaG / DnaI / DNA replication
Function / homology
Function and homology information


DNA primase DnaG / primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / DNA helicase activity / DNA-directed RNA polymerase complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-directed RNA polymerase activity / DNA replication / ATP hydrolysis activity ...DNA primase DnaG / primosome complex / DNA 5'-3' helicase / DNA replication, synthesis of primer / DNA helicase activity / DNA-directed RNA polymerase complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-directed RNA polymerase activity / DNA replication / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Primosomal DnaI, N-terminal / Primosomal protein DnaI N-terminus / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria ...Primosomal DnaI, N-terminal / Primosomal protein DnaI N-terminus / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / DNA primase, DnaB-helicase binding domain / DnaB-helicase binding domain of primase / Zinc finger, CHC2-type / DNA primase, DnaG / DNA primase, catalytic core, N-terminal / DNA primase DnaG, bacteria / Bacterial DnaG primase, TOPRIM domain / DNA primase, catalytic core, N-terminal domain superfamily / : / CHC2 zinc finger / DNA primase catalytic core, N-terminal domain / zinc finger / DNA Primase, CHC2-type zinc finger / DNA helicase, DnaB type / Toprim-like / DNA helicase, DnaB-like, N-terminal / DnaB-like helicase N terminal domain / DNA helicase, DnaB-like, N-terminal domain superfamily / DNA helicase DnaB, N-terminal/DNA primase DnaG, C-terminal / DnaB-like helicase C terminal domain / DNA helicase, DnaB-like, C-terminal / Superfamily 4 helicase domain profile. / TOPRIM / DEAD-box subfamily ATP-dependent helicases signature. / Toprim domain profile. / TOPRIM domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replicative helicase loader DnaI / Replicative DNA helicase DnaB / DNA primase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
Bacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.1 Å
AuthorsLiu, B. / Eliason, W.K. / Steitz, T.A.
CitationJournal: Nat Commun / Year: 2013
Title: Structure of a helicase-helicase loader complex reveals insights into the mechanism of bacterial primosome assembly.
Authors: Liu, B. / Eliason, W.K. / Steitz, T.A.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicative helicase
B: Replicative helicase
C: Replicative helicase
D: Replicative helicase
E: Replicative helicase
F: Replicative helicase
G: DNA primase
H: DNA primase
I: DNA primase
J: Primosomal protein DnaI
K: Primosomal protein DnaI
L: Primosomal protein DnaI
M: Primosomal protein DnaI
N: Primosomal protein DnaI
O: Primosomal protein DnaI


Theoretical massNumber of molelcules
Total (without water)576,53315
Polymers576,53315
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)229.055, 229.055, 364.294
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
Replicative helicase / Replicative helicase DnaB


Mass: 50699.445 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: dnaB / Plasmid: pET21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X4C9
#2: Protein DNA primase / DnaG Primase


Mass: 16796.490 Da / Num. of mol.: 3 / Fragment: Helicase Binding Domain (UNP residues 455-597)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: dnaG / Plasmid: pET21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9X4D0
#3: Protein
Primosomal protein DnaI / Helicase loader DnaI


Mass: 36991.152 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU28980, dnaI, ytxA / Plasmid: pET21d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P06567
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.79 Å3/Da / Density % sol: 74.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 8
Details: 11-13% w/v PEG3350, 0.2 M lithium sulfate, 50 mM TRIS, pH 8.0-8.3, VAPOR DIFFUSION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2010 / Details: mirrors
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 6→50 Å / Num. all: 26476 / Num. obs: 26476 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rsym value: 0.175 / Net I/σ(I): 3.7
Reflection shellResolution: 6→6.21 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 0.5 / Num. unique all: 2472 / Rsym value: 1 / % possible all: 90.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.1→20 Å / Cor.coef. Fo:Fc: 0.768 / Cor.coef. Fo:Fc free: 0.73 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 3.614 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.39154 974 5.1 %RANDOM
Rwork0.37906 ---
obs0.37968 17944 72.27 %-
all-17944 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 140.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 6.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31981 0 0 0 31981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02232391
X-RAY DIFFRACTIONr_angle_refined_deg1.391.97743641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09453977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39224.6291508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.256156056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.74215228
X-RAY DIFFRACTIONr_chiral_restr0.0890.25023
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02123892
X-RAY DIFFRACTIONr_mcbond_it0.1751.520082
X-RAY DIFFRACTIONr_mcangle_it0.315232325
X-RAY DIFFRACTIONr_scbond_it0.121312309
X-RAY DIFFRACTIONr_scangle_it0.2274.511316
LS refinement shellResolution: 6.1→6.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.773 8 -
Rwork0.865 123 -
all-131 -
obs--7.33 %

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